


Waiting For Him To Notice

by pinkdiamonds



Category: Stargate Atlantis
Genre: Angst, Denial, M/M, Misunderstandings, Romance, Sentient Atlantis
Language: English
Status: Completed
Published: 2014-07-15
Updated: 2014-07-15
Packaged: 2018-02-09 01:19:19
Rating: Explicit
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 3,819
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/1963569
Author URL: https://archiveofourown.org/users/pinkdiamonds/pseuds/pinkdiamonds
Summary: <blockquote class="userstuff">
              <p>John was just waiting for him to notice…</p>
            </blockquote>





	Waiting For Him To Notice

### Six Months Ago

Although there were still a few stray hive ships in Pegasus, the vast majority of the Wraith had committed to what would become known as the final battle of the war. Sheppard’s team and their discovery of a cache of four ZPM’s, along with the discovery of an Ancient manufacturing facility on a long abandoned planet with a broken Stargate had turned the tide in favor of the human populations. When the last hive ship engaged in the battle had been destroyed, John refused to relinquish the control chair and he landed Atlantis, his eyes searching out McKay, before collapsing.

The party waited for 72 hours while he recovered in the infirmary. In the meantime, Atlantis notified their allies as well as their enemies in the Pegasus galaxy -- who then spread the word of the Wraith defeat far and wide. By the time John was released dozens of planets had sent representatives laden with gifts. They were anxious to be friends with the people who had given them back their lives. They also wanted to make sure that Sheppard and Atlantis would be taking care of those few stray hives.

The party would go down in Atlantis history as one of the largest, longest, and loudest. The party went on for nearly four days, as the inhabitants of Atlantis were loath to turn anyone away. John had Rodney shield the labs and living quarters so only their own people could access them. He opened up a few large storage areas and had them supplied with cots and sleeping bags for the unexpected guests. 

He then made a token appearance at the party, where he was greeted with cheers, handshakes, and too many sloppy kisses to count. It was several hours before he was able to sneak out and hole up in an empty room way on the other side of Atlantis. He brought a sleeping bag, his tablet, and enough MRE’s to last for a few days as he planned just how he was going to eradicate the remaining Wraith.

John knew this should be one of the highlights of his life, but the roll call of the dead was constantly with him. That and the vision of Rodney and Keller wrapped around each other. Before he’d come here to write up his reports and work out tactical details, John had put Lorne in charge of the city, telling him he would be completely unavailable for a few days.

During the five days it took John to come to terms with this new normal, Rodney had tried to call him on his radio fifty-eight times. Woolsey had tried twice, Ronon once, and Teyla not at all. He answered Woolsey’s second call (which came on the third day) and ignored everyone else. He tried to prepare himself for the review he knew was coming from either the SGC or the IOA or both, and figured his chance of remaining the military commander of Atlantis was a little less than 20 percent.

When John finally returned to duty, it was to controlled chaos as the scientists were discovering and learning all about the new and shiny systems that had become available once the city had enough power. Rodney was in geek heaven and obviously pissed at John for ignoring him. He let John know in no uncertain terms that his presence was not welcome in the labs.

John retreated, knowing this was the perfect excuse to begin pulling back from McKay. Over the next few weeks, the only time he saw Rodney was during meetings for “Operation Mop-Up” as it had been dubbed, and during meal times where he was forced to watch as Rodney and Keller sat together a few tables away and ignored everyone but each other. It hurt him on a level that nothing had prepared him for.

Within weeks of the last major battle, Atlantis teams began Wraith baiting and then taking out the last remaining hives. Rodney had asked to be replaced on John’s team, and Sheppard had readily agreed. The need for McKay’s genius was not needed for Operation Mop-Up; he’d given the teams everything they needed in the way of tech to eradicate the last of the Wraith. And, if he had to listen to McKay extol the virtues of Keller, he thought he’d end up shooting either Rodney or himself.

When the last hive had been destroyed and John had brought all of his people home, there was no party awaiting the victorious men and women. Allies were busy rebuilding their worlds and Atlantis personnel were too busy trying to figure out technology so advanced it seemed like magic. There was, however, a message from the SGC informing them that General O’Neill, Dr. Jackson, Colonels Carter and Mitchell, and Teal’c would be coming through the Stargate in a week in order to discuss Atlantis’ new mandate as well as new personnel, both military and civilian.

John spent the week visiting all the secret places in Atlantis that he’d grown to love.

### Three Weeks Ago

The SGC personnel stepped through the ‘gate onto Atlantis bearing gifts. They pushed through cases of champagne and boxes of Godiva chocolates. John looked around for McKay; surprised he wasn’t there to greet his own personal goddess, Samantha Carter, and to grab his share of Godiva’s. O’Neill, Carter, and Mitchell were wearing dress blues, Jackson was wearing a blue suit, and Teal’c was in ceremonial robes.

Woolsey, understanding the subtle nuances of protocol, had insisted on a formal dinner and asked that all Atlantis personnel that were planning to attend to dress formally. The kitchen staff had been working for the last two days to prepare a suitably impressive feast.

The visitors were shown to their quarters and then escorted to a large room. A round table, big enough to fit the visitors, Richard, John, Teyla, Ronon, Rodney, Jennifer, Lorne, and Radek was centrally placed, with smaller tables scattered throughout the room and on the balcony. The lighting was subdued, casting interesting shadows around the room.

O’Neill, Carter, Jackson, Mitchell, Teal’c, Radek, and Richard were already seated and deep in conversation when John and most of his team arrived. Lorne joined them shortly as the room began to fill up. The only people missing were Rodney and Jennifer, and John wondered if they would even bother to show, although he couldn’t imagine McKay missing out on a good meal and champagne.

John was catching up on gossip at the SGC with O’Neill and Jackson when Rodney finally made his appearance. Dressed in a black suit with a plum shirt and tie, and wearing Keller on his arm, he looked good. Better than good; he looked liked he’d just walked out of one of John’s wet dreams. Keller was dressed in a clingy black gown and together they made a stunning pair, looking more like a power Hollywood couple than the CSO and CMO of an alien outpost. 

Blatantly eying McKay up and down, John settled on the smug smirk gracing the astrophysicist’s face. Ignoring everyone for the moment, Rodney focused on Carter. “Hello, Colonel Carter. You remember Dr. Keller,” he said breathlessly, and then paused dramatically. “My fiancé,” he gloated, thrusting Jennifer’s hand in front of her face.

Both Daniel and Teyla saw John pale. He quickly got himself together, adding his congratulations to all the others. He failed to see the surprised and covert glances being directed his way or between Jack and Daniel, Samantha and Cam, Teyla and Ronon, and Zelenka and Lorne. He also failed to hear the somewhat halfhearted and reserved congratulations the others were offering to Rodney and Jennifer.

John was hurt that Rodney hadn’t even discussed this with him. It wasn’t totally unexpected, but it still hurt. John knew this new development changed everything. He had hoped to be allowed to remain on Atlantis even if he wasn’t going to be the one in charge. He had no idea what his new orders were, but they no longer mattered. John decided within seconds that he was going to retire. A house on the ocean and endless days of surfing were looking like paradise right about now.

The rest of the night passed in a blur for John. He stuck to a single glass of champagne, nursing it through toast after toast till it was flat and warm. He watched as Rodney and Jennifer made their way from table to table announcing their engagement, never noticing the confused looks thrown his way after McKay and Keller had moved on to the next group of people.

He left as soon as he was able, snagging a bottle of champagne. He made sure to say goodnight to O’Neill, who kindly gave him two days downtime.

~*~

Rodney gave Jack and company a map of the areas that had been thoroughly vetted and that were deemed safe, and sent them on their way along with Richard and a team of five marines.

Teal’c had little interest in questioning scientists or seeing labs and could be found in the gym sparring with Ronon and the marines.

The SGC contingent met each night to discuss their findings. What they found was a well-run base, filled with bright energetic people who enjoyed their work. Sheppard was not only respected by his men and the scientists, he was nearly revered. There wasn’t a person living on the city that didn’t understand that he would give his life for theirs. He made them feel safe.

As for McKay, he, too, was well respected, even if he wasn’t always liked. Pulling off miracle after miracle and saving the collective asses of the expedition time after time had garnered Rodney the sort of respect that had eluded him when he was younger. The military was protective of him and the scientists recognized that he had a way of thinking that few others had. Put simply, whether they liked him or not, every person on the city was glad to have McKay on the job when the shit hit the fan.

O’Neill knew if he could get Keller out of the picture Sheppard and McKay would run the city well, making the most out of all the tech just waiting to be discovered. Atlantis would be in careful and loving hands and ultimately the waiting discoveries would be used to help the peoples of two galaxies.

~*~

A few nights before they were set to leave, Daniel lay in Jack’s arms when he asked, “Have you made a decision yet?”

“Of course. But McKay getting engaged changes things,” Jack answered. “We have no way of knowing for sure which way he’s gonna jump. He wants to be on the city part time. I’m inclined to tell him no just to force his hand.”

“Rumor has it that his relationship with Keller is fairly recent and totally unexpected,” Daniel said, snuggling deeper into Jack’s arms and yawning.

“Yeah, I caught that. I wonder why Sheppard never made a move? Anyone with eyes knows those two have been dancing around each other since Antarctica.” Jack noted. He tightened his arms around his lover. “If I have to, I’ll ask the city to intervene,” Jack laughed. Most people without a strong natural gene failed to realize the extent of the city’s sentience, which would work in his favor.

“Don’t you think that abusing your position just a little, Jack?”

“Probably, but the SGC and the IOA want Sheppard and McKay in charge of the city. Since everything we’ve been asked to look at checks out okay, that’s exactly what’s going to happen if I have anything to say about it. Even the President is on board. McKay shacking up with Keller throws a monkey wrench into those plans. But, I have a feeling it’s just a matter of throwing Sheppard and McKay together and letting nature take its course,” Jack proclaimed. “Of course, I think we’d better have a fire hose ready to separate those two once they get going,” Jack laughed.

“What about Keller? Don’t you feel at all bad about breaking up her and Rodney?” Daniel asked.

“She’s young, she’s beautiful, she’s brilliant, and she doesn’t deserve to be saddled with McKay. She’ll land on her feet,” Jack noted. “Besides, how long do you think it would be before McKay reverted to his usual charming self and made her regret marrying him?”

Laughing, Daniel replied, “Point.”

“Let’s go to sleep, Danny. We’ll sort out Sheppard and McKay’s love life tomorrow.”

~*~

The next day, Jack requested the company of Sheppard and McKay in the chair room. Although given his rank, it was really more of an order than a request, something both John and Rodney knew.

Sheppard insisted that Carson be on hand to monitor the General as well. Jack was in good health and a very vital man, but sitting in the chair was taxing. Jack put up with all the fussing, reminding both the doctor and Daniel that he wasn’t taking the city for a ride or to war.

Jack leaned back in the chair and within moments made contact with Atlantis. He opened his mind and let her see his plans for the city along with his intent for John and Rodney. She touched his mind gently, giving him the solution he was looking for.

The men watching Jack were puzzled by the grin on his face. Generally, sitting in the control chair meant crisis of one kind or another and expressions usually were grim and focused.

Jack spent an hour in the chair as Atlantis shared her own secrets and hopes for the future of the city. When he disconnected, he admitted to being tired and announced his intent to take the rest of the day off. He ordered Sheppard and McKay to meet him in the mess at 0900 for a bit of exploring based on some buildings Atlantis had showed him. He left the room with Daniel, leaving John, Rodney, and Carson to speculate on his experience in the chair.

~*~

Sheppard and McKay were eating when Jack and Daniel finally showed up a full fifteen minutes late. They both wore the smug air of men that had been recently laid and laid well. John refused to look at Rodney, and tried to stem his jealousy. He just wanted to get through the next few days and then go back through the gate with O’Neill and get on with his life. He’d been packing his few belongings, and had written a few letters in order to explain his decision to leave Atlantis. He realized Teyla would understand, but he also knew how much he’d be hurting Ronon. 

“Good morning, Sheppard, McKay,” Jack addressed the two men. All was right in his world and it showed. He folded his long body into a chair and leisurely began eating his reconstituted eggs and pancakes, as he leered at his lover.

Blushing, Daniel inhaled his first cup of coffee before nibbling at his toast, ignoring Jack’s leer. He shifted his backpack filled with water and snacks. It was a good thing Jack had a reputation for toting snacks around the city. As he had a number of other things to carry, he intended on giving it to McKay.

When all the men had finished eating, Jack led the way to the nearest transporter and entered coordinates unfamiliar to both John and Rodney. They exited at a non-discreet hallway, one that could be anywhere on Atlantis. Jack and Daniel allowed Sheppard and McKay to take the lead and shortly they arrived at an open door.

Jack encouraged John and Rodney to go on ahead to check out the obviously bare room.

~*~

The door locked behind John and Rodney, and then faded from sight. It took them seconds to realize they’d been separated from O’Neill and Jackson.

John clicked his mic. “General O’Neill? Are you and Dr. Jackson okay?”

“Yeah, we’re just fine, Sheppard. Atlantis isn’t going to let you and McKay out until you’ve got your shit together,” Jack replied.

“Sir?” John questioned.

“My gene is nearly as strong as yours, Sheppard. I arranged this when I sat in the control chair,” Jack said, the smirk very clear in his voice.

“Fuck,” John whispered. “General, this is a monumentally bad idea.” When there was no answer, John turned to Rodney ordering, “Get us out of here, McKay!”

“Already on it, Colonel,” Rodney answered. “Except there isn’t anything for me to work on. The door we came through is gone. Maybe you should just ask Atlantis nicely,” Rodney said, his tone sarcastic.

John slid down the wall, mentally screaming fuck over and over.

“Oh relax, Colonel. I realize that I’m the last person you want to be lost with, but I can promise you it won’t be for long,” Rodney informed his former team member. He then tried raising Radek. When that failed, he went through his entire staff with the same results. “Maybe you should try Lorne,” the scientist suggested.

When John was unable to raise anyone either, he understood that they were well and truly stuck until O’Neill was satisfied.

Rodney soon joined John on the floor. He went through the pack and ferreted out two power bars, offering one to John. After he’d taken a bite, he turned to the other man. “I guess this is where I tell you that when O’Neill and company go back, I’ll be joining them,” Rodney confessed. “I floated the idea to him a few days ago.”

John’s eyes widened slightly, and he moved for a gun that wasn’t there. “Alright, who the fuck are you, and what have you done with McKay?”

“What? I’m not allowed to have a fucking life, Colonel?”

“Of course you are. But you’re like some kind of pod person lately, McKay. Just who do you think you’re fooling? You know you won’t be happy on Earth,” John spit out in anger.

“It won’t be full time. I’ll spend a week in Atlantis every four to six weeks,” Rodney explained. “That way I can keep my hand in things, and Jennifer can do whatever it is she wants to do. You know she’s wanted to go home for a while now,” he finished.

“And who are you doing this for? You? Or her? We both know what’s going to happen – you’ll do that for a year and then it’ll be two days every three months until you never come back, “ John said bleakly.

“It isn’t like we won’t get to see each other, John. You’re my best friend, or you were, and you’ll always be welcome in my home,” Rodney begged for understanding.

“Wow, thanks, McKay. But, no thanks. I’ll be leaving as well. Except I’ll be leaving for good, and if there’s any justice in the world, I’ll never see you again for the whole rest of my life,” John stated bluntly.

“You wanna tell me what’s got your fucking panties in a twist, Colonel?”

“Maybe I just want you to be happy and I don’t think going back to Earth is going to accomplish that. Maybe seeing you try so hard to be what Keller expects you to be is starting to get on my fucking nerves. If she doesn’t want you for who you really are, maybe she isn’t the right person for you,” John listed. “You deserve someone who’s gonna love you, warts and all, Rodney.”

“Yeah, because they were lining up for me. And what do you mean you’re leaving Atlantis? This is your home!” McKay insisted, focusing on what he considered the most important point.

“Think, Rodney. O’Neill is here to review and decide who’s going to be in charge of the military. It won’t be me. As for my reasons for leaving, it’s none of your damn business,” Sheppard said.

Rising to pace, Rodney began muttering to himself. “You know what? It is my business. We’re supposed to be friends and I think I deserve to know why you’re leaving,” Rodney finally said.

“No,” John disagreed. “You don’t have the right. Not any more.” John took a bite of his power bar, chewing thoughtfully. “Why are you trying so hard with Keller anyway?” he asked curiously.

Turning bleak eyes John’s way, Rodney admitted, “Because for once I actually stood a chance.”

Laughing bitterly, John asked, “Is that what you really think?”

“You don't understand, John!” Rodney shouted.

“Then make me understand, Rodney!” John shouted back. “Make me understand,” he finished in a whisper.

And Rodney grabbed the front of Sheppard’s t-shirt, and hauled John up and into his arms pushing him up against the wall, kissing him with years of pent up passion, need, love, desperation, and nothing left to lose.

John’s arms snaked around Rodney, holding on tight as he kissed back with an equal amount of passion, need, love, and desperation.

Panting, Rodney thrust a leg in between John’s, gratified to feel an answering hard on grinding against his thigh. His mouth moved over John’s jaw and neck, kissing and gently biting. 

"I love you, John."

"I know. I’ve been waiting for you to notice."

"What the hell, Sheppard? I confess my love to you, and all you say is, 'I know?'"

"What? I was being truthful! You have all the subtlety of a charging rhino," John murmured between soft sucking kisses and deftly opening Rodney’s pants.

“Don’t you have something to say to me?” Rodney groaned as John’s hand made its way into his boxers and began stroking.

“Yeah. Get busy, it’s called mutual masturbation,” John grunted.

McKay’s clever hands found their target and John began pushing his cock into the warmth of the big hand holding him.

The two men kissed and a light sheen of sweat dewed their bodies. Coherent conversation was halted as whispered words of encouragement and love took over. John came with a deep and throaty moan moments before Rodney.

John leaned his head against the wall and smiled, his hands caressing the nape of Rodney’s neck.

“So, do you have anything to say to me now?” McKay sniped.

“Umm. You need to break up with Keller,” John drawled.

“Was planning that as soon as we get out of here,” Rodney acknowledged.

“You also need to tell O’Neill you’ll be staying,” Sheppard ordered.

“You’ll be staying as well?” the scientist questioned.

“Haven’t turned in my papers yet. I was going to wait until the last possible second,” came the soft answer. Turning serious, John said, “You also have to stop driving me crazy and proposing to women who can’t possibly love you more than I do, Rodney.”

“You love me?” Rodney prodded.

In answer, John kissed the man in his arms. “I also want you to move in with me being that we’re both packed and all. We’ll look for a place as soon as you’re done with Keller.”

“John…”

“Yes, Rodney. I love you.”

 

The End


End file.
